Tags

Type your tag names separated by a space and hit enter

Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China.
Mol Ecol Resour. 2014 Jan; 14(1):79-86.ME

Abstract

Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are invasive species and listed as US federally injurious species under the Lacy Act. They have established populations in much of the Mississippi River Basin (MRB; Mississippi, Illinois, and Missouri rivers) and are capable of producing fertile hybrids and complex introgression. Characterizing the composition of this admixture requires a large set of high-quality, evolutionarily conserved, diagnostic genetic markers to aid in the identification and management of these species in the midst of morphological ambiguity. Restriction site-associated DNA (RAD) sequencing of 45 barcoded bighead and silver carp from the United States and China produced reads that were aligned to the silver carp transcriptome yielded 261 candidate single nucleotide polymorphisms (SNPs) with fixed allelic differences between the two species. We selected the highest quality 112 SNP loci for validation using 194 putative pure-species and F1 hybrids from the MRB and putative bighead carp and silver carp pure species from China (Amur, Pearl and Yangtze rivers). Fifty SNPs were omitted due to design/amplification failure or lack of diagnostic utility. A total of 57 species-diagnostic SNPs conserved between carp species in US and Chinese rivers were identified; 32 were annotated to functional gene loci. Twenty-seven of the 181 (15%) putative pure species were identified as hybrid backcrosses after validation, including three backcrosses from the Amur River, where hybridization has not been documented previously. The 57 SNPs identified through RAD sequencing provide a diagnostic tool to detect population admixture and to identify hybrid and pure-species Asian carps in the United States and China.

Authors+Show Affiliations

Department of Biological Sciences, Western Illinois University, 1 University Circle, Macomb, IL, 61455, USA; Illinois Natural History Survey, 1816 S. Oak Street, Champaign, IL, 61820, USA.No affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info availableNo affiliation info available

Pub Type(s)

Evaluation Study
Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

23957862

Citation

Lamer, James T., et al. "Restriction Site-associated DNA Sequencing Generates High-quality Single Nucleotide Polymorphisms for Assessing Hybridization Between Bighead and Silver Carp in the United States and China." Molecular Ecology Resources, vol. 14, no. 1, 2014, pp. 79-86.
Lamer JT, Sass GG, Boone JQ, et al. Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China. Mol Ecol Resour. 2014;14(1):79-86.
Lamer, J. T., Sass, G. G., Boone, J. Q., Arbieva, Z. H., Green, S. J., & Epifanio, J. M. (2014). Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China. Molecular Ecology Resources, 14(1), 79-86. https://doi.org/10.1111/1755-0998.12152
Lamer JT, et al. Restriction Site-associated DNA Sequencing Generates High-quality Single Nucleotide Polymorphisms for Assessing Hybridization Between Bighead and Silver Carp in the United States and China. Mol Ecol Resour. 2014;14(1):79-86. PubMed PMID: 23957862.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Restriction site-associated DNA sequencing generates high-quality single nucleotide polymorphisms for assessing hybridization between bighead and silver carp in the United States and China. AU - Lamer,James T, AU - Sass,Greg G, AU - Boone,Jason Q, AU - Arbieva,Zarema H, AU - Green,Stefan J, AU - Epifanio,John M, Y1 - 2013/08/20/ PY - 2013/03/20/received PY - 2013/06/25/revised PY - 2013/06/30/accepted PY - 2013/8/21/entrez PY - 2013/8/21/pubmed PY - 2014/7/26/medline KW - Asian carp KW - RAD sequencing KW - SNP KW - hybridization KW - introgression KW - invasive species SP - 79 EP - 86 JF - Molecular ecology resources JO - Mol Ecol Resour VL - 14 IS - 1 N2 - Bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) are invasive species and listed as US federally injurious species under the Lacy Act. They have established populations in much of the Mississippi River Basin (MRB; Mississippi, Illinois, and Missouri rivers) and are capable of producing fertile hybrids and complex introgression. Characterizing the composition of this admixture requires a large set of high-quality, evolutionarily conserved, diagnostic genetic markers to aid in the identification and management of these species in the midst of morphological ambiguity. Restriction site-associated DNA (RAD) sequencing of 45 barcoded bighead and silver carp from the United States and China produced reads that were aligned to the silver carp transcriptome yielded 261 candidate single nucleotide polymorphisms (SNPs) with fixed allelic differences between the two species. We selected the highest quality 112 SNP loci for validation using 194 putative pure-species and F1 hybrids from the MRB and putative bighead carp and silver carp pure species from China (Amur, Pearl and Yangtze rivers). Fifty SNPs were omitted due to design/amplification failure or lack of diagnostic utility. A total of 57 species-diagnostic SNPs conserved between carp species in US and Chinese rivers were identified; 32 were annotated to functional gene loci. Twenty-seven of the 181 (15%) putative pure species were identified as hybrid backcrosses after validation, including three backcrosses from the Amur River, where hybridization has not been documented previously. The 57 SNPs identified through RAD sequencing provide a diagnostic tool to detect population admixture and to identify hybrid and pure-species Asian carps in the United States and China. SN - 1755-0998 UR - https://www.unboundmedicine.com/medline/citation/23957862/Restriction_site_associated_DNA_sequencing_generates_high_quality_single_nucleotide_polymorphisms_for_assessing_hybridization_between_bighead_and_silver_carp_in_the_United_States_and_China_ L2 - https://doi.org/10.1111/1755-0998.12152 DB - PRIME DP - Unbound Medicine ER -